Hey! You might want to constrain the bond between the 2 protein chains.
G *Thank you* *Gangotri Dey* Postdoctoral Associate Rutgers University New Brunswick Chemistry and Chemical Biology 174 Frelinghuysen Road, Piscataway, NJ 08854 Phone: +16092162254 On Fri, Jul 21, 2017 at 8:56 AM, Sneha Vishwanath < snehavishwanat...@gmail.com> wrote: > Dear all > > I am simulating a dimeric protein, with each subunit bound to a small > molecule. During the simulation, one of the ligands is dissociating from > the chain and moving all around the chain while the same ligand remains > bound to the chain during simulation. Experiments show that the ligand > binds to both the subunit which is further supported by the experimental > structure of the protein-ligand complex (which I have used for the > simulation). The simulation is for 50 ns and it usually starts dissociating > after 10 ns. > > Any thoughts on why could it be happening and how it can be circumvented? > Any help would be useful. > > Thanks in advance. > > Regards > Sneha Vishwanath > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.